Molec的ular Dynamics__ Simulation.pptVIP

Molecular DynamicsSimulation(a brief introduction) A Digital Laboratory “In the real world, this could eventually mean that most chemical experiments are conducted inside the silicon of chips instead of the glassware of laboratories. Turn off that Bunsen burner; it will not be wanted in ten years.” - The Economist, reporting on the work of the 1998 Chemistry Nobel Prize Awardees A Different Type of Simulation Many Physically-Based Simulations model easily observable real world phenomena. Molecular Dynamics Simulations model things too small for us to observe directly. Why Not Quantum Mechanics? Classical Mechanics Instead of using Quantum mechanics, we can use classical Newtonian mechanics to model our system. This is a simplification of what is actually going on, and is therefore less accurate. To alleviate this problem, we use numbers derived from QM for the constants in our classical equations. Molecular Modeling For each atom in every molecule, we need: Position (r) Momentum (m + v) Charge (q) Bond information (which atoms, bond angles, etc.) From Potential to Movement To run the simulation, we need the force on each particle. We use the gradient of the potential energy function. Now we can find the acceleration. What is the Potential? A single atom will be affected by the potential energy functions of every atom in the system: Bonded Neighbors Non-Bonded Atoms (either other atoms in the same molecule, or atoms from different molecules) Non-Bonded Atoms There are two potential functions we need to be concerned about between non-bonded atoms: van der Waals Potential Electrostatic Potential The van der Waals Potential Atoms with no net electrostatic charge will still tend to attract each other at short distances, as long as they don’t get too close. Once the atoms are close enough to have overlapping electron clouds, they will repel each other with astounding force The van der Waals Potential One of the most widely used functions for